When the band begins to play: histone acetylation caught in the crossfire of gene control

Design and synthesis of mono and bicyclic tetrapeptides thioester as potent inhibitor of histone deacetylases

Inhibitors of histone deacetylases (HDACs) are a promising class of anticancer agents that have an effect on gene regulation. The naturally occurring cyclic depsipeptide FK228 containing disulfide and Largazole possessing thioester functionalities act as pro-drugs and share the same HDAC inhibition mechanism in cell. Inspired from these facts, we have reported bicyclic tetrapeptide disulfide HDAC inhibitors resembling FK228 with potent activity and enhanced selectivity. In the present study, we report the design and synthesis of several mono and bicyclic tetrapeptide thioester HDAC inhibitors that share the inhibition mechanism similar to Largazole. Most of the compounds showed HDAC1 and HDAC4 inhibition and p21 promoting activity in nanomolar ranges. Among these the monocyclic peptides 1, 2 and bicyclic peptide, 4 are notable demanding more advanced research to be promising anticancer drug candidates.

Rat hepatocyte suspensions as a suitable in vitro model for studying the biotransformation of histone deacetylase inhibitors

This paper focuses on the use of liver-derived in vitro systems for biotransformation studies during early drug development, as exemplified by the two molecules recently studied in our laboratory: Trichostatin A (TSA) and its structural analogue 5-(4-dimethylaminobenzoyl)aminovaleric acid hydroxamide (4-Me2N-BAVAH). Phase I biotransformation of TSA, a histone deacetylase inhibitor with promising antifibrotic and antitumoural properties, was investigated in liver microsomal (rat and human) and in hepatocyte (rat) suspensions. Within 40 minutes, 50 microM of TSA was completely metabolised by 2 x 10(6) hepatocytes/ml. Reduction of the hydroxamic acid function to its corresponding amide and N-demethylation were the two major phase I biotransformation pathways, while hydrolysis products of TSA were minor metabolites. Lower concentrations of TSA (5 microM and 25 microM) were N-demethylated faster. Liver microsomes, however, metabolised TSA incompletely with the formation of two major metabolites, N-mono- and N-didemethylated TSA. Unlike TSA, 4-Me2N-BAVAH (50 microM) could still be detected after 3 hours of incubation with 2 x 10(6) rat hepatocytes/ml suspension. Hydrolysis and reduction of the hydroxamic acid function to its corresponding acid and amide, respectively, were shown to be the major phase I biotransformation pathways. Lower concentrations of 4-Me2N-BAVAH were hydrolysed more readily. 4-Me2N-BAVAH and its metabolites were less subjected to N-demethylation than TSA.

Cloning, chromosomal characterization and FISH mapping of the NAD(+)-dependent histone deacetylase gene sirtuin 5 in the mouse

Sirtuin 5 (SIRT5) is a nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase, belonging to the silent information regulator 2 (Sir2) family of sirtuin histone deacetylases (sirtuins). The yeast Sir2 protein and its mammalian derivatives are important in epigenetic gene silencing, DNA repair and recombination, cell cycle, microtubule organization and in the regulation of aging. In mammals, 7 sirtuin isoforms have been identified to date of which three (SIRT3, SIRT4 and SIRT5) are localized in the mitochondria, which serve as the center of energy management and the initiation of cellular apoptosis. In the study presented herein, we report the genomic organization and chromosomal localization of the murine sirt5 gene. We have isolated and characterized the murine sirt5 genomic sequence, which spans a region of 24,449 bp and which has one single genomic locus. The murine sirt5 gene consists of 8 exons and encodes a 310-aa protein with a predictive mo-lecular weight of 34.1 kDa and an isoelectric point of 8.90. For the murine sirt5 gene only one single genomic locus has been identified. The gene has been localized to mouse chromosome 13A4 and is flanked by STS-marker 164522 (synonymous WI MRC-RH: 506859).

The sirtuins in the pathogenesis of cancer

Aging is the natural trace that time leaves behind on life during blossom and maturation, culminating in senescence and death. This process is accompanied by a decline in the healthy function of multiple organ systems, leading to increased incidence and mortality from diseases such as diabetes, cancer, cardiovascular disease, and neurodegeneration. Based on the fact that both sirtuin expression and activity appear to be upregulated in some types of cancer while they are being downregulated in others, there is quite some controversy stirring up as to the role of sirtuins, acting as cancer suppressors in some cases while under other circumstances they may promote cellular malignancy. It is therefore currently quite unclear as to what extent and under which particular circumstances sirtuin activators and/or inhibitors will find their place in the treatment of age-related disease and cancer. In this review, we take an effort to bring together the highlights of sirtuin research in order to shed some light on the mechanistic impact that sirtuins have on the pathogenesis of cellular malignancy.

Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies

The accuracy of molecular dynamics (MD) simulations is limited by the availability of parameters for the molecular system of interest. In most force fields, parameters of common chemical groups are already present. With the development of novel small organic molecules as probes to study biological systems, more chemical groups require parameterization. An azide group is often used in studies of biological systems but computational studies are still impeded by the lack of parameters. In this paper, we present a set of molecular mechanics (MM) parameters for aromatic and aliphatic azido groups, and their application in MD simulations of a photoaffinity probe currently used in our laboratory for mapping binding modes available in the active site of histone deacetylases. The parameters were developed for the generalized Amber force field (GAFF) using density functional theory (DFT) calculations at B3LYP 6-311G(d) level. The parameters were validated by geometry optimization and MD simulations.

A duplexed phenotypic screen for the simultaneous detection of inhibitors of the molecular chaperone heat shock protein 90 and modulators of cellular acetylation

Histone deacetylases (HDACs), histone acetyltransferases (HATs), and the molecular chaperone heat shock protein 90 (HSP90) are attractive anticancer drug targets. High-throughput screening plays a pivotal role in modern molecular mechanism-based drug discovery. Cell-based screens are particularly useful in that they identify compounds that are permeable and active against the selected target or pathway in a cellular context. We have previously developed time-resolved fluorescence cell immunosorbent assays (TRF-Cellisas) for compound screening and pharmacodynamic studies. These assays use a primary antibody to the single protein of interest and a matched secondary immunoglobulin labeled with an europium chelate (Eu). The availability of species-specific secondary antibodies labeled with different lanthanide chelates provides the potential for multiplexing this type of assay. The approach has been applied to the development of a 384-well duplexed cell-based screen to simultaneously detect compounds that induce the co-chaperone HSP70 as a molecular marker of potential inhibitors of HSP90 together with those that modulate cellular acetylation (i.e., potential inhibitors of histone deacetylase or histone acetyltransferase activity). The duplexed assay proved reliable in high-throughput format and approximately 64,000 compounds were screened. Following evaluation in secondary assays, 3 of 13 hits from the HSP70 arm were confirmed. Two of these directly inhibited the intrinsic ATPase activity of HSP90 whereas the third seems to have a different mechanism of action. In the acetylation arm, two compounds increased cellular acetylation, one of which inhibited histone deacetylase activity. A third compound decreased cellular histone acetylation, potentially through a novel mechanism of action.

The cloning and characterization of the histone acetyltransferase human homolog Dmel\TIP60 in Drosophila melanogaster: Dmel\TIP60 is essential for multicellular development

Chromatin packaging directly influences gene programming as it permits only certain portions of the genome to be activated in any given developmental stage, cell, and tissue type. Histone acetyltransferases (HATs) are a key class of chromatin regulatory proteins that mediate such developmental chromatin control; however, their specific roles during multicellular development remain unclear. Here, we report the first isolation and developmental characterization of a Drosophila HAT gene (Dmel\TIP60) that is the homolog of the human HAT gene TIP60. We show that Dmel\TIP60 is differentially expressed during Drosophila development, with transcript levels significantly peaking during embryogenesis. We further demonstrate that reducing endogenous Dmel\TIP60 expression in Drosophila embryonic cells by RNAi results in cellular defects and lethality. Finally, using a GAL4-targeted RNAi system in Drosophila, we show that ubiquitous or mesoderm/muscle-specific reduction of Dmel\TIP60 expression results in lethality during fly development. Our results suggest a mechanism for HAT regulation involving developmental control of HAT expression profiles and show that Dmel\TIP60 is essential for multicellular development. Significantly, our inducible and targeted HAT knockdown system in Drosophila now provides a powerful tool for effectively studying the roles of TIP60 in specific tissues and cell types during development.

Abnormalities of chromatin in tumor cells

Nuclear morphometric descriptors such as nuclear size, shape, DNA content and chromatin organization are used by pathologists as diagnostic markers for cancer. Tumorigenesis involves a series of poorly understood morphological changes that lead to the development of hyperplasia, dysplasia, in situ carcinoma, invasive carcinoma, and in many instances finally metastatic carcinoma. Nuclei from different stages of disease progression exhibit changes in shape and the reorganization of chromatin, which appears to correlate with malignancy. Multistep tumorigenesis is a process that results from alterations in the function of DNA. These alterations result from stable genetic changes, including those of tumor suppressor genes, oncogenes and DNA stability genes, and potentially reversible epigenetic changes, which are modifications in gene function without a change in the DNA sequence. DNA methylation and histone modifications are two epigenetic mechanisms that are altered in cancer cells. The impact of genetic (e.g., mutations in Rb and ras family) and epigenetic alterations with a focus on histone modifications on chromatin structure and function in cancer cells are reviewed here.

Chemistry and biology of mercaptoacetamides as novel histone deacetylase inhibitors

A series of mercaptoacetamides were designed and synthesized as novel histone deacetylase inhibitors with the aid of modeling. Their ability to inhibit HDAC activity and their effects on cancer cell growth were investigated. Some compounds exhibit better HDAC inhibitory activity than SAHA.

Trichostatin A-induced histone acetylation causes decondensation of interphase chromatin

The effect of trichostatin A (TSA)-induced histone acetylation on the interphase chromatin structure was visualized in vivo with a HeLa cell line stably expressing histone H2A, which was fused to enhanced yellow fluorescent protein. The globally increased histone acetylation caused a reversible decondensation of dense chromatin regions and led to a more homogeneous distribution. These structural changes were quantified by image correlation spectroscopy and by spatially resolved scaling analysis. The image analysis revealed that a chromatin reorganization on a length scale from 200 nm to >1 microm was induced consistent with the opening of condensed chromatin domains containing several Mb of DNA. The observed conformation changes could be assigned to the folding of chromatin during G1 phase by characterizing the effect of TSA on cell cycle progression and developing a protocol that allowed the identification of G1 phase cells on microscope coverslips. An analysis by flow cytometry showed that the addition of TSA led to a significant arrest of cells in S phase and induced apoptosis. The concentration dependence of both processes was studied.

Phase I study of oral CI-994 in combination with gemcitabine in treatment of patients with advanced cancer

PURPOSE

The purpose of this study was to determine the maximum tolerated dose, pharmacokinetic profile, and evidence of antitumor activity of CI-994 used in combination with gemcitabine.

METHODS

This was a dose escalation trial in which gemcitabine (1,000 mg/m2) was given as a 30-minute infusion on days 1, 8, and 15 of a 28-day cycle. CI-994 was taken orally on consecutive days 1-21 at escalating doses of 2, 4, 6, and 8 mg/m2 per cohort (three patients/cohort). Plasma samples were collected on days 1 and 15 of course 1 and analyzed for CI-994 pharmacokinetic assessment.

RESULTS

Twenty patients with advanced cancer received a total of 76 courses of treatment. Dose-limitingtoxicity occurred at the 8-mg/ m2 dose. Four of seven patients experienced thrombocytopenia during the first cycle. Grade 4 thrombocytopenia was observed in three of 10 (30%) courses at 8 mg/m2. In contrast, only two of 28 (7%) courses at 6 mg/m2 were associated with grade 4 thrombocytopenia. Pharmacokinetic analysis indicated that absorption of CI-994 was rapid, with peak plasma concentrations occurring at the first sample 2 hours after dosing. Two patients achieved a minor response, 12 had stable disease (median duration, 105 days), four had progressive disease, and two were not evaluable.

CONCLUSIONS

The 6-mg/m2 dose of CI-994 (p.o. x 21 days) was defined as the maximum tolerated dose that could safely be administered in combination with gemcitabine (1,000 mg/m2 i.v. on days 1, 8, and 15) during a 28-day cycle.

Major phase I biotransformation pathways of Trichostatin a in rat hepatocytes and in rat and human liver microsomes

Phase I biotransformation of Trichostatin A (TSA), a histone deacetylase inhibitor with promising antifibrotic and antitumoral properties, was investigated in rat and human liver microsomes and in suspensions of rat hepatocytes. TSA (50 micro M) was readily and completely metabolized by rat hepatocytes in suspension (2 x 10(6) cells/ml), whereafter its phase I metabolites were separated by high-performance liquid chromatography and detected with simultaneous UV and electrospray ionization mass spectrometry (ESI-MS). ESI tandem mass spectrometry (ESI-MS/MS) was used to identify the metabolites. Two major phase I biotransformation pathways in rat hepatocytes were shown to be N-demethylation and reduction of the hydroxamic acid function to its corresponding amide. N-monodemethylated TSA and TSA amide were preferentially formed during the first 20 min of exposure, and N-monodemethylated TSA amide appeared as the main metabolite after a 30 min incubation period. At this time, virtually all TSA had been metabolized. Trichostatic acid, N-monodemethylated Trichostatic acid, and N-didemethylated TSA were identified as minor metabolites. Longer incubation led to the formation of N-didemethylated TSA amide as the main metabolite. Lower concentrations of TSA (5 and 25 micro M) formed relatively higher amounts of N-demethylated, nonreduced metabolites. Incubations of TSA with rat and human microsomal suspensions, however, led to an incomplete biotransformation with the formation of two major metabolites, N-mono- and N-didemethylated TSA. Traces of Trichostatic acid, TSA amide, N-mono- and N-didemethylated TSA amide were also detected. This study is the first to show that TSA undergoes intensive phase I biotransformation in rat hepatocytes. This has important consequences for its potential development as a drug, since rapid biotransformation resulting in a short exposure to the pharmacologically active parent compound, and a complex mixture of metabolites is usually not desired. Further biotransformation studies of TSA and structural analogs with antitumoral and antifibrotic properties need to be performed in cultured intact hepatocytes, in particular since one of the major phase I biotransformation pathways is catalyzed by nonmicrosomal enzymes.

Chromosomal organization and localization of the human histone deacetylase 9 gene (HDAC9)

Epigenetically mediated modulation of gene promoter function through histone acetylation modifying enzymes, which regulate the acetylation state of histone proteins and other promoter-bound transcription factors, is increasingly appreciated as a key component in the regulation of reversible gene expression. While histone acetyltransferases (HATs), which are frequently part of multisubunit coactivator complexes, lead to the relaxation of chromatin structure and transcriptional activation, histone deacetylases (HDACs) tend to associate with multisubunit corepressor complexes, which result in chromatin condensation and transcriptional repression of specific target genes. We have isolated and characterized the human HDAC9 genomic sequence, which spans a region of 458 kb and which has one single chromosomal locus. Determination of the exon-intron splice-junctions established that HDAC9 is encoded by 23 exons ranging in size from 22 bp (exon 1) to 264 bp (exon 11). Characterization of the 5' flanking genomic region revealed that the human HDAC9 promoter lacks both the canonical TATA and CCAAT boxes; CpG elements are missing. The human HDAC9 open reading frame is 3036 bp long and encodes a 1011 aa protein with a predictive molecular weight of 111.3 kDa and an isoelectric point of 6.41. Fluorescence in situ hybridization analysis localized the human HDAC9 gene to chromosome 7p21, a region which has been associated particularly with the pathogenesis of gynecological tumors.

Inhibitors of human histone deacetylase: synthesis and enzyme and cellular activity of straight chain hydroxamates

Inhibitors of histone deacetylase (HDAC) have been shown to induce terminal differentiation of human tumor cell lines and to have antitumor effects in vivo. We have prepared analogues of suberoylanilide hydroxamic acid (SAHA) and trichostatin A and have evaluated them in a human HDAC enzyme inhibition assay, a p21(waf1) (p21) promoter assay, and in monolayer growth inhibition assays. One compound, 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]-benzamide, was found to affect the growth of a panel of eight human tumor cell lines differentially.

Chromosomal organization and localization of the human histone deacetylase 5 gene (HDAC5)

Histone deacetylases (HDACs) are important participants in the remodeling of chromatin structure and in the regulation of eukaryotic proliferation and differentiation. We have isolated and characterized the human HDAC5 genomic sequence, which spans a region of 39,138 bp and which has one single chromosomal locus. Determination of the exon-intron splice junctions established that HDAC5 is encoded by 26 exons ranging in size from 22 bp (exon 1) to 285 bp (exon 12). Characterization of the 5' flanking genomic region revealed that the human HDAC5 promoter lacks both the canonical TATA and CCAAT boxes. The human HDAC5 mRNA encodes a 1122 aa protein with a predictive molecular mass of 121.9 kDa and an isoelectric point of 5.84. Fluorescence in situ hybridization analysis localized the human HDAC5 gene to chromosome 17q21, a region which is characterized by frequent gains and losses of chromosomal material in several types of cancer.